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Move to pyproject_toml + package cleanup - #549

Merged

mihaic merged 207 commits into

masterfrom

pyproject_toml

Nov 15, 2024

Merged

Move to pyproject_toml + package cleanup#549
mihaic merged 207 commits into
masterfrom
pyproject_toml

Commits on Apr 29, 2024
- Move to pyproject.toml
  davidt0x
  committed
  54e1c57
- Move to pyproject.toml
  davidt0x
  committed
  61a4a01
- Unpin tensorflow
  davidt0x
  committed
  e3d3b9b
- Bump min Python version
  davidt0x
  committed
  ab20a2a
- Lower pin on tf for tf probability
  davidt0x
  committed
  dac2c6b
- Disable cancel in progress of fails for now.
  davidt0x
  committed
  9f01a6f
- Disable cancel in progress of fails for now.
  davidt0x
  committed
  daa123a
Commits on Apr 30, 2024
- Remove numpy upper pin
  davidt0x
  committed
  fb1192f
- brew install libomp on macos
  davidt0x
  committed
  766efeb
- scipy.signal is no scipy.signal.windows
  davidt0x
  committed
  e922b61
- tensorflow_probability now requires extras [tf] lol
  davidt0x
  committed
  a9cd400
- Disable codecov for now.
  davidt0x
  committed
  f701edc
- Debug macos
  davidt0x
  committed
  f21b877
- Fixes for finding openMP macos
  davidt0x
  committed
  8d5e34e
- Disable debug.
  davidt0x
  committed
  a6ee9ab
- Install conda on macos
  davidt0x
  committed
  e3dd9c9
- Turn off fail fast for conda, for debug.
  davidt0x
  committed
  06706e5
- Remove numpy upper pin in conda recipe.
  davidt0x
  committed
  7e7fd76
- Delete everything from setup.cfg
  davidt0x
  committed
  a6f60ee
- Remove setup.cfg completely, move flake8 config to .flake8
  davidt0x
  committed
  d8dc1d7
- Specify .flake8 config
  davidt0x
  committed
  1ce5283
- Make coverage concurrency multi string
  davidt0x
  committed
  a856828
Commits on Jun 10, 2024
- Convert to scikit-build-core
  davidt0x
  committed
  be3fa93
- Specify build type as Release
  davidt0x
  committed
  8d22da1
- Add openmp for fcma and factoranalysis
  davidt0x
  committed
  baeeedc
- Add cibuildwheel setup
  davidt0x
  committed
  498a004
- Add cibuildwheel to workflow.
  davidt0x
  committed
  77ba5e4
- Turn off fail fast for now.
  davidt0x
  committed
  f9f4652
- Test linux windows now
  davidt0x
  committed
  72bfc51
- Add mpi4py-mpich install for cibuildwheel
  davidt0x
  committed
  a472439
- Fix mpich install command.
  davidt0x
  committed
  c21fd27
- cibuildwheel fixes
  davidt0x
  committed
  2c19f09
- Remove unused sys time include from tfa
  davidt0x
  committed
  2b41421
- cibuildwheel fixes
  davidt0x
  committed
  eca5215
- Fixes in tfa_extension.cpp for windows.
  davidt0x
  committed
  f37a0d4
- Fixes for cibuildwheel
  davidt0x
  committed
  51c3fd9
- Fix race condition
  davidt0x
  committed
  a755b80
- Windows fixes for fcma_extension
  davidt0x
  committed
  8116339
- cibuildwheel fixes
  davidt0x
  committed
  f5c4151
- Cibuildwheels fixes
  davidt0x
  committed
  8a7a5d2
Commits on Jun 11, 2024
- fixes
  davidt0x
  committed
  08c0103
- fixes
  davidt0x
  committed
  72ee3cb
- fixes
  davidt0x
  committed
  ab3894a
- asdasd
  davidt0x
  committed
  9b4a6a2
- fixes
  davidt0x
  committed
  c50230d
- fixes
  davidt0x
  committed
  6f2c16f
- Change np.bool to bool.
  davidt0x
  committed
  d8e411f
- Fixes
  davidt0x
  committed
  ff29893
- Add script for building libomp
  davidt0x
  committed
  ae9413c
- More np.bool changes
  davidt0x
  committed
  c6942f4
- Fix libomp build
  davidt0x
  committed
  7d6529f
- Add exec permission to build omp script.
  davidt0x
  committed
  7a2068f
Commits on Sep 9, 2024
- Add check for OpenMP in CMakeLists.txt
  davidt0x
  committed
  a4e4abf
- Make scikit build core verbose
  davidt0x
  committed
  c9f3579
- Mark some ssrm tests as xfail.
  davidt0x
  committed
  a96493f
- Construct ragged arrays as dtype=object in srm.
  davidt0x
  committed
  bece98f
- Fix pip install command.
  davidt0x
  committed
  7f33fbc
Commits on Sep 30, 2024
- Fix for fastsrm and ragged numpy arrays.
  davidt0x
  committed
  7c3c829
- Style cleanups.
  davidt0x
  committed
  676ca41
- Fix issue with scipy 1.6
  davidt0x
  committed
  f62dbc0
- Exclude Python 3.12 and above from wheels.
  davidt0x
  committed
  1a67ba4
- Remove unused omp.h include in fcma.
  davidt0x
  committed
  6722efa
- Fix for windows cibuild.
  davidt0x
  committed
  d1aecff
- Disable 3.8 for now.
  davidt0x
  committed
  c48c9d2
- Remove omp.h from tfa as well.
  davidt0x
  committed
  9c884ed
- Build only 64 bit wheels.
  davidt0x
  committed
  ca6403e
- Try to fix mpiexec path windows.
  davidt0x
  committed
  3379b25
- Setup mpi4py with action instead.
  davidt0x
  committed
  461fd2d
- Fix cibuildwheel config, archs instead of platforms.
  davidt0x
  committed
  d38d9ab
- Remove call to test at bottom of test_distributed_srm
  davidt0x
  committed
  7511886
- Explicitly set dtype on randint
  davidt0x
  committed
  520649c
- Skip musllinux for now.
  davidt0x
  committed
  1732ff3
- Style cleanup.
  davidt0x
  committed
  e72bade
Commits on Oct 1, 2024
- Fix randint dtype issue on windows.
  davidt0x
  committed
  b3c6900
- Fix apt-get commands.
  davidt0x
  committed
  6a86744
- Try yum
  davidt0x
  committed
  07f58a8
- Try yum
  davidt0x
  committed
  50b0f77
- Remove pin on cibuildwheel
  davidt0x
  committed
  45bbf16
- Try disabling epel from yum
  davidt0x
  committed
  a4fe088
- More linux and windows fixes.
  davidt0x
  committed
  d690cbc
- More linux and windows fixes.
  davidt0x
  committed
  afabf12
Commits on Oct 2, 2024
- For linux cibuildwheel, build mpi4py wheel.
  davidt0x
  committed
  b1d5346
- Try using intel mpi for windows.
  davidt0x
  committed
  54044d1
- Handle escaping windows path in regex.
  davidt0x
  committed
  847fd91
- More windows and linux cibuildwheel fixes
  davidt0x
  committed
  935a797
- Dont install mpi4py wheel on linux.
  davidt0x
  committed
  c8b3e80
- Dont install mpi4py wheel on linux.
  davidt0x
  committed
  0a0537d
- Fixes for muslinux
  davidt0x
  committed
  5225f31
- Re-enable MPI for windows.
  davidt0x
  committed
  748be1e
- Skip muslinux
  davidt0x
  committed
  dc47760
- Remove theano dependency.
  davidt0x
  committed
  b11d953
- Try python 3.12 and above now with theano gone.
  davidt0x
  committed
  23d9c39
- Style cleanup
  davidt0x
  committed
  d6f8d1f
- Enable MPI again on windows. Drop Python 3.13.
  davidt0x
  committed
  69f88ec
- Actually skip musllinux.
  davidt0x
  committed
  cf9c1ae
- Fix a bunch of deprecation warnings.
  davidt0x
  committed
  cc8529d
- Attempt to fix conda build
  davidt0x
  committed
  3344931
Commits on Oct 3, 2024
- More removal of deprecated pkg_resources
  davidt0x
  committed
  3cbe981
- Make voxel selection tests deterministic.
  davidt0x
  committed
  1ca65b4
- Support specifying pool_size on SearchLight construction
  davidt0x
  committed
  200131e
- Use pytest.raises match syntax in test_htfa
  davidt0x
  committed
  8cd3be6
Commits on Oct 4, 2024
- Cleanup MPI tests.
  davidt0x
  committed
  7d217b7
- Try adding openmpi to PATH.
  davidt0x
  committed
  0c90478
- Fix openmpi path.
  davidt0x
  committed
  710699f
- Whoops, left this commented out.
  davidt0x
  committed
  0315663
- Style cleanups
  davidt0x
  committed
  fa64acd
- Fix test for Open MPI
  davidt0x
  committed
  b3bbdbb
- Debug linux openmpi install
  davidt0x
  committed
  df09ea5
- Another attempt to add mpi to PATH
  davidt0x
  committed
  e62802f
- Define __version__ in __init__.py
  davidt0x
  committed
  0087f6d
- Try add PATH to cibuildwheel linux environment.
  davidt0x
  committed
  d480480
- Try add PATH to cibuildwheel linux environment again.
  davidt0x
  committed
  652f4b6
- Add F401 for __init__.py flake8 ignore.
  davidt0x
  committed
  6ceee6c
- Add OMPI_ALLOW_RUN_AS_ROOT to linux environment,
  davidt0x
  committed
  99a6288
- Enable MPI run as root.
  davidt0x
  committed
  3049cf6
- Enable MPI run as root.
  davidt0x
  committed
  4c0b586
- Enable MPI run as root.
  davidt0x
  committed
  ab4ebe2
- Enable MPI run as root.
  davidt0x
  committed
  64fd4a2
- Fix indent
  davidt0x
  committed
  d1bf219
- Another workaround for old MPI
  davidt0x
  committed
  de50ef5
Commits on Oct 14, 2024
- Attempt to fix conda build
  davidt0x
  committed
  881338b
- No pytest-mpiexec in conda
  davidt0x
  committed
  bc178e1
- Hard code version
  davidt0x
  committed
  2fd0838
- Try to get version from setuptools_scm
  davidt0x
  committed
  a448189
- Try to get version from setuptools_scm
  davidt0x
  committed
  044b04f
- Try to get version from setuptools_scm
  davidt0x
  committed
  1920145
- Try to get version from setuptools_scm
  davidt0x
  committed
  cfedaae
- Try to get version from setuptools_scm
  davidt0x
  committed
  351d9b9
- Try to get version from setuptools_scm
  davidt0x
  committed
  6e191de
- Try to get version from setuptools_scm
  davidt0x
  committed
  15d80ae
- Try to get version from setuptools_scm
  davidt0x
  committed
  62b5479
- Try to get version from setuptools_scm
  davidt0x
  committed
  d67ce49
- Try to get version from setuptools_scm
  davidt0x
  committed
  4917a8f
- Try to get version from setuptools_scm
  davidt0x
  committed
  8862dda
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  4b6d769
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  1f05ea8
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  31650af
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  c10d6d4
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  3bc00a1
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  fb6257c
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  9166756
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  5cba769
- Add pytest-mpiexec plugin to source.
  davidt0x
  committed
  47d37f4
- Typo
  davidt0x
  committed
  019f2fc
- Typo
  davidt0x
  committed
  39a973b
- Refactor package to src layout
  davidt0x
  committed
  4e3c158
Commits on Oct 15, 2024
- Refactor package to src layout
  davidt0x
  committed
  af07070
- Try to install pymanopt in script
  davidt0x
  committed
  0b58413
- Try to install pymanopt in script
  davidt0x
  committed
  446bf76
- Re-add sim_parameters that were git ignored
  davidt0x
  committed
  365185c
- Another src refactor fix for docs.
  davidt0x
  committed
  969bc1f
- Remove MKL_THREADING_LAYER=GNU
  davidt0x
  committed
  3f0c13d
- Not sure why this got set to #!/bin/sh
  davidt0x
  committed
  a50c5c5
- Remove BRAINIAK_HOME
  davidt0x
  committed
  6f8d6b5
- Update some actions
  davidt0x
  committed
  08bc414
- Add windows and macos-13 to conda build
  davidt0x
  committed
  0a3e74d
- Cleanup conda build in actions
  davidt0x
  committed
  1d5630b
- Cleanup conda build in actions
  davidt0x
  committed
  ac476ad
- Cleanup conda build in actions
  davidt0x
  committed
  019d140
- Cleanup conda build in actions
  davidt0x
  committed
  16d6295
- Cleanup conda build in actions
  davidt0x
  committed
  f4dc4fa
- Fix condition for windows setuptools_scm
  davidt0x
  committed
  d0900ed
- Try to fix conda build command.
  davidt0x
  committed
  8c6948a
- Try to fix conda build command.
  davidt0x
  committed
  6ae4b15
- Try to fix conda build command.
  davidt0x
  committed
  80ffdeb
- Try to fix conda build command.
  davidt0x
  committed
  9ff4e93
- Try to fix conda build command.
  davidt0x
  committed
  1855244
- Try to fix conda build command.
  davidt0x
  committed
  b73cb22
- Try to fix conda build command.
  davidt0x
  committed
  e9ec71a
- Try to fix conda build command.
  davidt0x
  committed
  b134183
- Add fetch-depth: 0 to checkouts
  davidt0x
  committed
  0f6f16d
Commits on Oct 28, 2024
- Build OpenMP for macos wheels.
  davidt0x
  committed
  7690b75
- np.NaN to np.nan for numpy 2.0
  davidt0x
  committed
  104df55
- Fixes for numpy 2 np.linalg.solve changes.
  davidt0x
  committed
  706d244
- Flake8 fixes.
  davidt0x
  committed
  4f359fb
- Correct fix for numpy 2.
  davidt0x
  committed
  f4641a3
- Flake 8 fixes.
  davidt0x
  committed
  346630d
- Fix for numpy 2.
  davidt0x
  committed
  a4f8ef1
Commits on Oct 30, 2024
- Fix for numpy 2.
  davidt0x
  committed
  ddee651
- Remove THEANO_FLAGS.
  davidt0x
  committed
  d2a2cfe
Commits on Nov 13, 2024
- Cleanup tests workflow.
  davidt0x
  committed
  f039fd0
- Bump the lower pin on tensorflow.
  davidt0x
  committed
  07f025e
- Fix openmp setup on MacOS
  davidt0x
  committed
  e3d88c6
- Attempt to fix windows conda build
  davidt0x
  committed
  9ce91e4
- Upper pin on tables 3.9 in examples-requirements.txt
  davidt0x
  committed
  e96c8e5
- Drop tensorflow requirement conda windows.
  davidt0x
  committed
  0c5978c
- Remove PIP_NO_INDEX=False
  davidt0x
  committed
  3a32d13
- Drop nltools req.
  davidt0x
  committed
  4415e3d
- Add PIP_NO_INDEX to env.
  davidt0x
  committed
  716404b
- Put PIP_NO_INDEX back.
  davidt0x
  committed
  02bac2a
- Increase timeout on hfta test.
  davidt0x
  committed
  d87edb8
- Try again conda windows.
  davidt0x
  committed
  82b7fab
Commits on Nov 14, 2024
- Drop windows conda for now.
  davidt0x
  committed
  c41dcfa
- Fix INSTALL_NAME_DIR for openmp
  davidt0x
  committed
  f59c05a
- Put back lower pin on TF 2.16
  davidt0x
  committed
  7a58f26
- Upper pin of TFP.
  davidt0x
  committed
  6fcfd12
- Increase timeout to 120 on all mpi tests.
  davidt0x
  committed
  33dfbd4
- Refactor workflows into cd.yml and ci.yml
  davidt0x
  committed
  4e2da32
- Fix syntax error.
  davidt0x
  committed
  88545a2
- Fix syntax error.
  davidt0x
  committed
  51e0917
- Try msmpi on windows, having intelmpi issues.
  davidt0x
  committed
  ed095c1
Commits on Nov 15, 2024
- Uncomment uploading to conda and pypi.
  davidt0x
  committed
  b815a55
- Add windows tests.
  davidt0x
  committed
  826727f
- Use msmpi on windows.
  davidt0x
  committed
  fae6b09
- Merge branch 'master' of https://github.com/brainiak/brainiak into pyproject_toml
  davidt0x
  committed
  8b3189e
- Build wheels only on release or PR.
  davidt0x
  committed
  97366b5
- Add testing for Python 3.12 and conda build for 3.12
  davidt0x
  committed
  ba6e9de

Commits

Commits on Apr 29, 2024

Commits on Apr 30, 2024

Commits on Jun 10, 2024

Commits on Jun 11, 2024

Commits on Sep 9, 2024

Commits on Sep 30, 2024

Commits on Oct 1, 2024

Commits on Oct 2, 2024

Commits on Oct 3, 2024

Commits on Oct 4, 2024

Commits on Oct 14, 2024